Array-Array Expression Level Distance Plot for Device

Description

A false color display of between arrays distances, computed as the MAD of the M-values of each pair of arrays for the selected device.

Usage

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plotMAD(x,
        which      = "UnitName",
        transfo    = log2,
        col        = NULL,
        names      = "namepart",
        sort       = FALSE,
        bmar       = NULL,
        add.legend = FALSE,
        dev        = "screen",
        outfile    = "MADPlot",
        w          = 540,
        h          = 540,
        ...) 

Arguments

x

object of class ExprTreeSet.

which

type of probes to be used, for details see validData.

transfo

a valid function to transform the data, usually “log2”, or “0”.

col

vector of colors for plot, length is number of samples.

names

optional vector of sample names.

sort

logical, if TRUE the correlation matrix will be sorted decreasingly.

bmar

optional list for bottom margin and axis label magnification cex.axis.

add.legend

logical, if TRUE then a color bar will be drawn.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

...

optional arguments to be passed to plot.

Details

Produces a false color display, i.e. heatmap, of between array distances for slot data for an object of class ExprTreeSet, computed as the MAD of the M-values of each pair of arrays.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as mdaplot.

For bmar=NULL the default list bmar = list(b=6, cex.axis=1.0) will be used initially. However, both bottom margin and axis label magnification will be adjusted depending on the number of label characters and the number of smaples.

Author(s)

Christian Stratowa

See Also

madplot

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